User:David Canner/Sandbox good

How to Make Excellent Scenes
This is a list of tips and tricks to develop effective scenes for your pages. The scenes below were taken from the indicated pages.



Example from the page The Structure of PI3K:
Initial Scene (Reset) Although no crystal structure of PI3K with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. In this model, the headgroup of PIP2 is positioned in a cavity between the C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop. This puts the 5-phosphate of PIP2 near Lys 973 and the I-phosphate of ATP near Lys 807 and Lys 808. The basic residues Arg 947 and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed His 948 rotates to interact with PIP2, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3.

Example from the page The Structure of PI3K
Initial Scene (Reset) The alpha-A helix of NSH2 (residues 340-345) is anchored into  a cavity created by the C2 and Kinase domain interface. Helix α11K of the Kinase domain (residues 1017-1024) interacts with the alpha-A helix of nSH2. nSH2 interacts with the C2 domain through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong salt bridge between NSH2 Glu 349 and C2 residue Arg 357, and hydrogen bonds between NSH2 Glu 348 and C2 Glu 453 and Asp 454.

Example from the page The Structure of PI3K
Initial Scene (Reset) This loop in <scene name='User:David_Canner/Sandbox_P/Nsh2__and_helical_ligand_out/2'>the helical domain which contains the hotspots (residues 542-546) is located precisely where <scene name='User:David_Canner/Sandbox_P/Nsh2_ligand_just_ligand_full/1'> the phosphopeptide of NSH2 ligands, like PDGFR, bind to NSH2. The salt bridge formed between <scene name='User:David_Canner/Sandbox_P/Nsh2_disruption_of_salt/1'>Glu 542 and nSH2 is disrupted upon binding phosphorylated peptides like PDGFR, eliminating nSH2-mediated inhibition of p110α and activating the enzyme to phosphorylate PIP2 into PIP3.

Example from the page The Structure of PI3K:
<scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset) <scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>The alpha-A helix of NSH2 (residues 340-345) is anchored into <scene name='User:David_Canner/Sandbox_P/Nsh2_pocket/2'> a cavity created by the C2 and Kinase domain interface. Helix α11K of the <scene name='User:David_Canner/Sandbox_P/Kinase_domain_out/2'>Kinase domain (residues 1017-1024) <scene name='User:David_Canner/Sandbox_P/Nsh2_kianse/1'>interacts with the alpha-A helix of nSH2. nSH2 interacts with the <scene name='User:David_Canner/Sandbox_P/C2_out/3'>C2 domain through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong <scene name='User:David_Canner/Sandbox_P/Nsh2_charge_charge/3'>salt bridge between NSH2 Glu 349 and C2 residue Arg 357, and hydrogen bonds between NSH2 Glu 348 and C2 Glu 453 and Asp 454.

Example from the page PI3K Activation, Inhibition, & Medical Implications:
<scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset) LY294002, a competitive inhibitor of ATP binding in the PI3K kinase domain, was first discovered by scientists at Eli Lilly. Quercetin, Myricetin & Staurosporine are natural compounds which broadly inhibit protein kinases. Understanding how ATP binds to the ATP binding site <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>within the kinase domain of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to <scene name='User:David_Canner/Sandbox_P/Inhibitor_atp/5'>ATP (1e8x), <scene name='User:David_Canner/Sandbox_P/Inhibitor_wortmannin/7'>Wortmannin (1e7u), <scene name='User:David_Canner/Sandbox_P/Inhibitor_ly294002/2'>LY294002 (1e7v), <scene name='User:David_Canner/Sandbox_P/Inhibitor_quer/2'>Quercetin (1e8w), <scene name='User:David_Canner/Sandbox_P/Inhibitor_staur/1'>Staurosporine (1e8z), <scene name='User:David_Canner/Sandbox_P/Inhibitor_myrice/1'>Myricetin (1e90).

Example from the page VirE1-VirE2:
<scene name='User:David_Canner/Sandbox_Shira/Opening/2'>Initial Scene (Reset) In <scene name='User:David_Canner/Sandbox_Shira/Opening_3/2'>the heterodimer, the two folded domains of <scene name='User:David_Canner/Sandbox_Shira/Clamp_4/2'>VirE2 clamp. tightly around the single alpha-helix of VirE1. Both <scene name='User:David_Canner/Sandbox_Shira/Pocket/4'>electrostatic and hydrophobic interactions with VirE1 cement the two domains of VirE2 into a “locked” conformation where the flexible extended linker joining these two independent VirE2 domains does not constrain their relative orientation. Most of the interactions are electrostatic, involving <scene name='User:David_Canner/Sandbox_Shira/Elec/3'>salt bridges between residues R168, K248, H315, R367 and K471 from VirE2 and N34, D40, E42, E45, E47 and N48 from VirE1. The <scene name='User:David_Canner/Sandbox_Shira/Acidic/4'>acidic residues of VirE1 contribute to its strong electronegative surface resembling that of ssDNA. VirE2 can bind alternatively to VirE1 or to ssDNA. The acidic nature common to both substrates suggests that they bind via electrostatic interactions to a common region of VirE2.

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